The way I usually do it is by manipulating hydrogens directly in the molecule
object:
mol.DeleteHydrogens()
mol.AddHydrogens(polaronly=False, correctForPh=True, pH=7.4)
The only caveat is that this method is not as reliable as the command line.
The outcome might be different from what obtained when using 'obabel' directly,
and does not seem to be very robust (e.g., unreasonable formal charges,
bonds...)
I suggest you to try with your molecules and double-check the output. Sometimes
performing these operations before adding hydrogens seem to help:
mol.UnsetFlag(openbabel.OB_PH_CORRECTED_MOL)
mol.SetAutomaticFormalCharge(True)
There are a few open issues on the matter on GitHub.
Hope this helps,
Stefano
On 4/17/19 1:29 AM, Tim Dudgeon wrote:
> Yes, but I don't see how that helps work out how to call it from Python.
> I was trying something like this:
>
>> obConversion.AddOption("p", obConversion.GENOPTIONS, "3.0")
> That seems vaguely consistent with how to set the option from Python given
> how the CLI option works, but unfortunately it doesn't seem to work.
>
> Tim
>
> On 15/04/2019 13:03, Noel O'Boyle wrote:
>> Hi Tim,
>>
>> Many of these options are just wrappers around API functions, so it's
>> worthwhile taking a look at the API documentation. In this case, here's the
>> link to the relevant docs:
>>
>> http://openbabel.org/api/2.3/classOpenBabel_1_1OBPhModel.shtml
>>
>> Regards,
>> - Noel
>>
>> On Thu, 11 Apr 2019 at 16:11, Tim Dudgeon <[email protected]
>> <mailto:[email protected]>> wrote:
>>
>> Another Python options question.
>> I can use the protonation option on the CLI:
>>
>> > echo "C1=C(NC=N1)C[C@@H](C(=O)O)N" | obabel -i smi -o mol -p 3
>> But I can't figure it out with the Python API:
>>
>> > import openbabel
>> >
>> > obConversion = openbabel.OBConversion()
>> > obConversion.SetInAndOutFormats("smi", "mol")
>> > mol = openbabel.OBMol()
>> > obConversion.AddOption("p", obConversion.GENOPTIONS, "3.0")
>> > obConversion.ReadString(mol, "C1=C(NC=N1)C[C@@H](C(=O)O)N")
>> > output = obConversion.WriteString(mol)
>> > print output
>> Output is generated but it's not protonated. Same if using OUTOPTIONS
>> instead of GENOPTIONS.
>>
>> Is the use of the options in Python documented anywhere?
>>
>>
>>
>>
>>
>> _______________________________________________
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>> <mailto:[email protected]>
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>>
>
>
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--
Stefano Forli, PhD
Assistant Professor
Dept. of Integrative Structural
and Computational Biology, MB-112A
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
tel: +1 (858)784-2055
fax: +1 (858)784-2860
email: [email protected]
http://www.scripps.edu/faculty/forli/
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